Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-12-01 Thread Phil Evans
It’s best to think of slicing as just sampling the 3D reciprocal space. Then in 
the absence of errors fine slicing will improve signal/noise by reducing the 
excess background under the peaks. However [Mueller M, Wang M, Schulze-Briese 
C. Acta Cryst (2012) D68, 42-56] show that there are diminishing returns from 
slicing the spot width into more than 4 or 5 slices, and with finer slicing 
handling more data may be a nuisance. Shutterless data collection with modern 
pixel array detectors introduces very little noise / image, so this argument 
holds.

With older systems, there is a compromise with

1. shutter jitter, depending on the speed of data collection compared to the 
shutter speed
2. goniometer accuracy, to handle the stop/start synchronised with the shutter
3. read-out noise of the detector
4. reducing the background under the spots

1-3 favour thicker slices, 4 favours thinner

Judging the balance with shuttered collection is complicated, but the advantage 
of shutterless data collection with fast detectors is clear

Phil

> On 1 Dec 2016, at 04:42, Edward A. Berry  wrote:
> 
> On 11/30/2016 10:16 PM, Keller, Jacob wrote:
>>> If you fine slice and everything is then a partial, isn't that *more* 
>>> sensitive to lack of synchronization between the shutter and rotation axis 
>>> than the wide-frame method where there's a larger proportion of fulls that 
>>> don't approach the frame edges (in rotation space) ?  Especially if you're 
>>> 3D profile fitting ?
>> 
>> That is how the argument seems to go in Pflugrath 1999, but I would think 
>> that shutter jitter is a random error, so it would seem better to have 
>> several of these random errors for a given spot than just one. Perhaps 
>> measuring with high multiplicity would have the same averaging effect.
>> 
>>> Is fine slicing more or less beneficial at high resolutions relative to 
>>> lower ones ?
>> 
>> In terms of I/sigI, it seems to be the same proportional improvement across 
>> all resolutions. See Fig 4 of the Pflugrath 1999 paper.
>> 
>> JPK
> 
> I think the problem there is that, if the shutter jitter is random with a 
> constant sigma, it becomes a larger percent of the total exposure for that 
> frame. It would be like taking a 1ml pipetor with an error of 2% of full 
> scale, i.e. 20 ul. Because you want to average this out, you set it to 200 ul 
> and pipet 5 times. The sigma of that measurement would be sqrt(5) * 20 ul, I 
> think, so worse than doing it all in one shot. On the other hand if you take 
> a 200 ul pipet with sigma 2% of full scale or 4 ul, and take 5 times, the 
> error is sqrt(5) * 4 ul which is less than 20 ul.
> Of course this would not apply to reflections that are fully recorded on one 
> frame since they are not reflecting while the shutter is open/closing. Then 
> it would be only variation in background.
> 
>> 
>> Phil Jeffrey
>> 
>> Princeton
>> 
>> --
>> 
>> *From:*CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, 
>> Jacob [kell...@janelia.hhmi.org]
>> *Sent:* Wednesday, November 30, 2016 5:44 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK 
>> *Subject:* Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
>> Count Numbers
>> 
>> If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about 
>> half the time is spent measuring non-spot background noise under spots in 
>> phi, which is all lumped into the intensity measurement. Fine slicing 
>> reduces this. But I am conjecturing that there is also fine-slicing-mediated 
>> improvement due to averaging out things like shutter jitter, which would 
>> also be averaged out through plain ol’ multiplicity.
>> 
>> I guess a third equal-count dataset would be useful as well: one sweep with 
>> six-fold finer slicing. So it would be:
>> 
>> One sweep, 0.6 deg, 60s
>> 
>> Six sweeps, 0.6 deg, 10s
>> 
>> One sweep, 0.1 deg, 10s
>> 
>> Or something roughly similar. Who will arrange the bets?
>> 
>> JPK
>> 
>> 

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Edward A. Berry

On 11/30/2016 10:16 PM, Keller, Jacob wrote:

If you fine slice and everything is then a partial, isn't that *more* sensitive 
to lack of synchronization between the shutter and rotation axis than the 
wide-frame method where there's a larger proportion of fulls that don't 
approach the frame edges (in rotation space) ?  Especially if you're 3D profile 
fitting ?


That is how the argument seems to go in Pflugrath 1999, but I would think that 
shutter jitter is a random error, so it would seem better to have several of 
these random errors for a given spot than just one. Perhaps measuring with high 
multiplicity would have the same averaging effect.


Is fine slicing more or less beneficial at high resolutions relative to lower 
ones ?


In terms of I/sigI, it seems to be the same proportional improvement across all 
resolutions. See Fig 4 of the Pflugrath 1999 paper.

JPK


I think the problem there is that, if the shutter jitter is random with a 
constant sigma, it becomes a larger percent of the total exposure for that 
frame. It would be like taking a 1ml pipetor with an error of 2% of full scale, 
i.e. 20 ul. Because you want to average this out, you set it to 200 ul and 
pipet 5 times. The sigma of that measurement would be sqrt(5) * 20 ul, I think, 
so worse than doing it all in one shot. On the other hand if you take a 200 ul 
pipet with sigma 2% of full scale or 4 ul, and take 5 times, the error is 
sqrt(5) * 4 ul which is less than 20 ul.
Of course this would not apply to reflections that are fully recorded on one 
frame since they are not reflecting while the shutter is open/closing. Then it 
would be only variation in background.



Phil Jeffrey

Princeton

--

*From:*CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
*Sent:* Wednesday, November 30, 2016 5:44 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
Count Numbers

If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about 
half the time is spent measuring non-spot background noise under spots in phi, 
which is all lumped into the intensity measurement. Fine slicing reduces this. 
But I am conjecturing that there is also fine-slicing-mediated improvement due 
to averaging out things like shutter jitter, which would also be averaged out 
through plain ol’ multiplicity.

I guess a third equal-count dataset would be useful as well: one sweep with 
six-fold finer slicing. So it would be:

One sweep, 0.6 deg, 60s

Six sweeps, 0.6 deg, 10s

One sweep, 0.1 deg, 10s

Or something roughly similar. Who will arrange the bets?

JPK

*From:*Boaz Shaanan [mailto:bshaa...@bgu.ac.il]
*Sent:* Wednesday, November 30, 2016 5:19 PM
*To:* Keller, Jacob >; 
CCP4BB@JISCMAIL.AC.UK 
*Subject:* RE: Effects of Multiplicity and Fine Phi with Equivalent Count 
Numbers

Hi Jacob,

I may have missed completely your point but as far as my memory goes, the main 
argument in favour of fine slicing has always been reduction of the noise 
arising from incoherent scattering, which in the old days arose from the 
capillary, solvent, air, you name it. The noise reduction in fine slicing is 
achieved by shortening the exposure time per frame. This argument still holds 
today although the sources of incoherent scattering could be different. Of 
course, there are other reasons to go for fine slicing such as long axes and 
others. In any case it's the recommended method these days, and for good 
reasons, isn't it?

   Best regards,

Boaz

/Boaz Shaanan, Ph.D. //
/Dept. of Life Sciences /
/Ben-Gurion University of the Negev /
/Beer-Sheva 84105 /
/Israel /
//
/E-mail: bshaa...@bgu.ac.il /
/Phone: 972-8-647-2220  Skype: boaz.shaanan /
/Fax:   972-8-647-2992 or 972-8-646-1710 //

//


Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Keller, Jacob
I am wondering whether part of the benefit of fine slicing is really increased 
multiplicity in disguise. I have seen in papers that empirically things do not 
improve much (or can even get slightly worse) past 0.5*SigPhi, which is the 
XDS-defined version of mosaicity; according to MOSFLM’s definition of 
mosaicity, which is ~2-3 larger than that from XDS, this would correspond to 
~0.15-0.25 * mosaic spread (Mueller et al 2011). Accordingly, a crystal with 
MOSFLM mosaic spread of 0.6 would be best measured with ~0.1 deg oscillations, 
meaning, I think, that the spot would be measured at least six times as a 
partial, leading to some averaging of various errors from frame to frame.

JPK




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward 
Snell
Sent: Wednesday, November 30, 2016 8:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
Count Numbers


There is a very nice paper by Colin Nave on Matching X-ray beam and detector 
properties to protein crystals of different perfection​,J Synchrotron Radiat. 
2014  21, 537–546. Due to the spectral and geometric properties of in house 
sources there is probably no advantage with an oscillation below 0.2 degrees no 
matter how good the crystal is. A well conditioned beamline can gain an 
advantage from a very perfect crystal but once you cryocool them all bets are 
off. Make sure you consider the instrument resolution parameters (spectral and 
geometric divergence) and the actual crystal quality. As to resolution 
dependence, it all comes down to the source of the mosaicity, e.g. domain 
misalignment, imperfections, domain boundary effects and domain size. There is 
a rich literature around but speaking from first hand experience, it's not 
trivial to probe this area.



Cheers,



Eddie.


Edward Snell Ph.D.
President and CEO Hauptman-Woodward Medical Research Institute
Assistant Prof. Department of Structural Biology, University at Buffalo
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: 
esn...@hwi.buffalo.edu
Heisenberg was probably here!​

​


From: CCP4 bulletin board > 
on behalf of Jeffrey, Philip D. 
>
Sent: Wednesday, November 30, 2016 7:36 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
Count Numbers

Jacob,

If you fine slice and everything is then a partial, isn't that *more* sensitive 
to lack of synchronization between the shutter and rotation axis than the 
wide-frame method where there's a larger proportion of fulls that don't 
approach the frame edges (in rotation space) ?  Especially if you're 3D profile 
fitting ?

Is fine slicing more or less beneficial at high resolutions relative to lower 
ones ?

Phil Jeffrey
Princeton

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 5:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
Count Numbers
If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about 
half the time is spent measuring non-spot background noise under spots in phi, 
which is all lumped into the intensity measurement. Fine slicing reduces this. 
But I am conjecturing that there is also fine-slicing-mediated improvement due 
to averaging out things like shutter jitter, which would also be averaged out 
through plain ol’ multiplicity.

I guess a third equal-count dataset would be useful as well: one sweep with 
six-fold finer slicing. So it would be:

One sweep, 0.6 deg, 60s
Six sweeps, 0.6 deg, 10s
One sweep, 0.1 deg, 10s

Or something roughly similar. Who will arrange the bets?

JPK


From: Boaz Shaanan [mailto:bshaa...@bgu.ac.il]
Sent: Wednesday, November 30, 2016 5:19 PM
To: Keller, Jacob >; 
CCP4BB@JISCMAIL.AC.UK
Subject: RE: Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

Hi Jacob,

I may have missed completely your point but as far as my memory goes, the main 
argument in favour of fine slicing has always been reduction of the noise 
arising from incoherent scattering, which in the old days arose from the 
capillary, solvent, air, you name it. The noise reduction in fine slicing is 
achieved by shortening the exposure time per frame. This argument still holds 
today although the sources of incoherent scattering could be different. Of 
course, there are other reasons to go for fine slicing such as long axes and 
others. In any case it's the recommended method these days, and 

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Keller, Jacob
>If you fine slice and everything is then a partial, isn't that *more* 
>sensitive to lack of synchronization between the shutter and rotation axis 
>than the wide-frame method where there's a larger proportion of fulls that 
>don't approach the frame edges (in rotation space) ?  Especially if you're 3D 
>profile fitting ?

That is how the argument seems to go in Pflugrath 1999, but I would think that 
shutter jitter is a random error, so it would seem better to have several of 
these random errors for a given spot than just one. Perhaps measuring with high 
multiplicity would have the same averaging effect.

>Is fine slicing more or less beneficial at high resolutions relative to lower 
>ones ?

In terms of I/sigI, it seems to be the same proportional improvement across all 
resolutions. See Fig 4 of the Pflugrath 1999 paper.

JPK




Phil Jeffrey
Princeton

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 5:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
Count Numbers
If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about 
half the time is spent measuring non-spot background noise under spots in phi, 
which is all lumped into the intensity measurement. Fine slicing reduces this. 
But I am conjecturing that there is also fine-slicing-mediated improvement due 
to averaging out things like shutter jitter, which would also be averaged out 
through plain ol' multiplicity.

I guess a third equal-count dataset would be useful as well: one sweep with 
six-fold finer slicing. So it would be:

One sweep, 0.6 deg, 60s
Six sweeps, 0.6 deg, 10s
One sweep, 0.1 deg, 10s

Or something roughly similar. Who will arrange the bets?

JPK


From: Boaz Shaanan [mailto:bshaa...@bgu.ac.il]
Sent: Wednesday, November 30, 2016 5:19 PM
To: Keller, Jacob >; 
CCP4BB@JISCMAIL.AC.UK
Subject: RE: Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

Hi Jacob,

I may have missed completely your point but as far as my memory goes, the main 
argument in favour of fine slicing has always been reduction of the noise 
arising from incoherent scattering, which in the old days arose from the 
capillary, solvent, air, you name it. The noise reduction in fine slicing is 
achieved by shortening the exposure time per frame. This argument still holds 
today although the sources of incoherent scattering could be different. Of 
course, there are other reasons to go for fine slicing such as long axes and 
others. In any case it's the recommended method these days, and for good 
reasons, isn't it?

  Best regards,

   Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 11:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count 
Numbers
Dear Crystallographers,

I am curious whether the observed effects of fine phi slicing might in part or 
in toto be due to simply higher "pseudo-multiplicity." In other words, under 
normal experimental conditions, does simply increasing the number of 
measurements increase the signal and improve precision, even with the same 
number of total counts in the dataset?

As such, I am looking for a paper which, like Pflugrath's 1999 paper, compares 
two data sets with equivalent total counts but, in this case, different 
multiplicities. For example, is a single sweep with 0.5 degree 60s exposures 
empirically, in real practice, equivalent statistically to six passes with 0.5 
degree 10s frames? Better? Worse? Our home source has been donated away to 
Connecticut, so I can't do this experiment myself anymore.

All the best,

Jacob Keller


***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***



Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Edward Snell
There is a very nice paper by Colin Nave on Matching X-ray beam and detector 
properties to protein crystals of different perfection​,J Synchrotron Radiat. 
2014  21, 537–546. Due to the spectral and geometric properties of in house 
sources there is probably no advantage with an oscillation below 0.2 degrees no 
matter how good the crystal is. A well conditioned beamline can gain an 
advantage from a very perfect crystal but once you cryocool them all bets are 
off. Make sure you consider the instrument resolution parameters (spectral and 
geometric divergence) and the actual crystal quality. As to resolution 
dependence, it all comes down to the source of the mosaicity, e.g. domain 
misalignment, imperfections, domain boundary effects and domain size. There is 
a rich literature around but speaking from first hand experience, it's not 
trivial to probe this area.


Cheers,


Eddie.


Edward Snell Ph.D.
President and CEO Hauptman-Woodward Medical Research Institute
Assistant Prof. Department of Structural Biology, University at Buffalo
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Heisenberg was probably here!​

​


From: CCP4 bulletin board  on behalf of Jeffrey, Philip 
D. 
Sent: Wednesday, November 30, 2016 7:36 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
Count Numbers

Jacob,

If you fine slice and everything is then a partial, isn't that *more* sensitive 
to lack of synchronization between the shutter and rotation axis than the 
wide-frame method where there's a larger proportion of fulls that don't 
approach the frame edges (in rotation space) ?  Especially if you're 3D profile 
fitting ?

Is fine slicing more or less beneficial at high resolutions relative to lower 
ones ?

Phil Jeffrey
Princeton

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 5:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
Count Numbers

If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about 
half the time is spent measuring non-spot background noise under spots in phi, 
which is all lumped into the intensity measurement. Fine slicing reduces this. 
But I am conjecturing that there is also fine-slicing-mediated improvement due 
to averaging out things like shutter jitter, which would also be averaged out 
through plain ol’ multiplicity.

I guess a third equal-count dataset would be useful as well: one sweep with 
six-fold finer slicing. So it would be:

One sweep, 0.6 deg, 60s
Six sweeps, 0.6 deg, 10s
One sweep, 0.1 deg, 10s

Or something roughly similar. Who will arrange the bets?

JPK


From: Boaz Shaanan [mailto:bshaa...@bgu.ac.il]
Sent: Wednesday, November 30, 2016 5:19 PM
To: Keller, Jacob ; CCP4BB@JISCMAIL.AC.UK
Subject: RE: Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

Hi Jacob,

I may have missed completely your point but as far as my memory goes, the main 
argument in favour of fine slicing has always been reduction of the noise 
arising from incoherent scattering, which in the old days arose from the 
capillary, solvent, air, you name it. The noise reduction in fine slicing is 
achieved by shortening the exposure time per frame. This argument still holds 
today although the sources of incoherent scattering could be different. Of 
course, there are other reasons to go for fine slicing such as long axes and 
others. In any case it's the recommended method these days, and for good 
reasons, isn't it?

  Best regards,

   Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 11:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count 
Numbers
Dear Crystallographers,

I am curious whether the observed effects of fine phi slicing might in part or 
in toto be due to simply higher “pseudo-multiplicity.” In other words, under 
normal experimental conditions, does simply increasing the number of 
measurements increase the signal and improve precision, even with the same 
number of total counts in the dataset?

As such, I am looking for a paper which, like Pflugrath’s 1999 paper, compares 
two data sets with equivalent total counts but, in this case, different 

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Jeffrey, Philip D.
Jacob,

If you fine slice and everything is then a partial, isn't that *more* sensitive 
to lack of synchronization between the shutter and rotation axis than the 
wide-frame method where there's a larger proportion of fulls that don't 
approach the frame edges (in rotation space) ?  Especially if you're 3D profile 
fitting ?

Is fine slicing more or less beneficial at high resolutions relative to lower 
ones ?

Phil Jeffrey
Princeton

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 5:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent 
Count Numbers

If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about 
half the time is spent measuring non-spot background noise under spots in phi, 
which is all lumped into the intensity measurement. Fine slicing reduces this. 
But I am conjecturing that there is also fine-slicing-mediated improvement due 
to averaging out things like shutter jitter, which would also be averaged out 
through plain ol’ multiplicity.

I guess a third equal-count dataset would be useful as well: one sweep with 
six-fold finer slicing. So it would be:

One sweep, 0.6 deg, 60s
Six sweeps, 0.6 deg, 10s
One sweep, 0.1 deg, 10s

Or something roughly similar. Who will arrange the bets?

JPK


From: Boaz Shaanan [mailto:bshaa...@bgu.ac.il]
Sent: Wednesday, November 30, 2016 5:19 PM
To: Keller, Jacob ; CCP4BB@JISCMAIL.AC.UK
Subject: RE: Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

Hi Jacob,

I may have missed completely your point but as far as my memory goes, the main 
argument in favour of fine slicing has always been reduction of the noise 
arising from incoherent scattering, which in the old days arose from the 
capillary, solvent, air, you name it. The noise reduction in fine slicing is 
achieved by shortening the exposure time per frame. This argument still holds 
today although the sources of incoherent scattering could be different. Of 
course, there are other reasons to go for fine slicing such as long axes and 
others. In any case it's the recommended method these days, and for good 
reasons, isn't it?

  Best regards,

   Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 11:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count 
Numbers
Dear Crystallographers,

I am curious whether the observed effects of fine phi slicing might in part or 
in toto be due to simply higher “pseudo-multiplicity.” In other words, under 
normal experimental conditions, does simply increasing the number of 
measurements increase the signal and improve precision, even with the same 
number of total counts in the dataset?

As such, I am looking for a paper which, like Pflugrath’s 1999 paper, compares 
two data sets with equivalent total counts but, in this case, different 
multiplicities. For example, is a single sweep with 0.5 degree 60s exposures 
empirically, in real practice, equivalent statistically to six passes with 0.5 
degree 10s frames? Better? Worse? Our home source has been donated away to 
Connecticut, so I can’t do this experiment myself anymore.

All the best,

Jacob Keller


***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***



Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Keller, Jacob
If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about 
half the time is spent measuring non-spot background noise under spots in phi, 
which is all lumped into the intensity measurement. Fine slicing reduces this. 
But I am conjecturing that there is also fine-slicing-mediated improvement due 
to averaging out things like shutter jitter, which would also be averaged out 
through plain ol' multiplicity.

I guess a third equal-count dataset would be useful as well: one sweep with 
six-fold finer slicing. So it would be:

One sweep, 0.6 deg, 60s
Six sweeps, 0.6 deg, 10s
One sweep, 0.1 deg, 10s

Or something roughly similar. Who will arrange the bets?

JPK


From: Boaz Shaanan [mailto:bshaa...@bgu.ac.il]
Sent: Wednesday, November 30, 2016 5:19 PM
To: Keller, Jacob ; CCP4BB@JISCMAIL.AC.UK
Subject: RE: Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

Hi Jacob,

I may have missed completely your point but as far as my memory goes, the main 
argument in favour of fine slicing has always been reduction of the noise 
arising from incoherent scattering, which in the old days arose from the 
capillary, solvent, air, you name it. The noise reduction in fine slicing is 
achieved by shortening the exposure time per frame. This argument still holds 
today although the sources of incoherent scattering could be different. Of 
course, there are other reasons to go for fine slicing such as long axes and 
others. In any case it's the recommended method these days, and for good 
reasons, isn't it?

  Best regards,

   Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob 
[kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 11:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count 
Numbers
Dear Crystallographers,

I am curious whether the observed effects of fine phi slicing might in part or 
in toto be due to simply higher "pseudo-multiplicity." In other words, under 
normal experimental conditions, does simply increasing the number of 
measurements increase the signal and improve precision, even with the same 
number of total counts in the dataset?

As such, I am looking for a paper which, like Pflugrath's 1999 paper, compares 
two data sets with equivalent total counts but, in this case, different 
multiplicities. For example, is a single sweep with 0.5 degree 60s exposures 
empirically, in real practice, equivalent statistically to six passes with 0.5 
degree 10s frames? Better? Worse? Our home source has been donated away to 
Connecticut, so I can't do this experiment myself anymore.

All the best,

Jacob Keller


***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***



Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Boaz Shaanan



Hi Jacob,


I may have missed completely your point but as far as my memory goes, the main argument in favour of fine slicing has always been reduction of the noise arising from incoherent scattering, which in the old days arose from the capillary, solvent, air, you
 name it. The noise reduction in fine slicing is achieved by shortening the exposure time per frame. This argument still holds today although the sources of incoherent scattering could be different. Of course, there are other reasons to go for fine slicing
 such as long axes and others. In any case it's the recommended method these days, and for good reasons, isn't it?


  Best regards,


                   Boaz
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 








From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob [kell...@janelia.hhmi.org]
Sent: Wednesday, November 30, 2016 11:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers





Dear Crystallographers,
 
I am curious whether the observed effects of fine phi slicing might in part or in toto be due to simply higher “pseudo-multiplicity.” In other words, under normal experimental conditions, does simply increasing the number of measurements
 increase the signal and improve precision, even with the same number of total counts in the dataset?
 
As such, I am looking for a paper which, like Pflugrath’s 1999 paper, compares two data sets with equivalent total counts but, in this case, different multiplicities. For example, is a single sweep with 0.5 degree 60s exposures empirically,
 in real practice, equivalent statistically to six passes with 0.5 degree 10s frames? Better? Worse? Our home source has been donated away to Connecticut, so I can’t do this experiment myself anymore.
 
All the best,
 
Jacob Keller
 
 
***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email:
kell...@janelia.hhmi.org
***
 









[ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

2016-11-30 Thread Keller, Jacob
Dear Crystallographers,

I am curious whether the observed effects of fine phi slicing might in part or 
in toto be due to simply higher "pseudo-multiplicity." In other words, under 
normal experimental conditions, does simply increasing the number of 
measurements increase the signal and improve precision, even with the same 
number of total counts in the dataset?

As such, I am looking for a paper which, like Pflugrath's 1999 paper, compares 
two data sets with equivalent total counts but, in this case, different 
multiplicities. For example, is a single sweep with 0.5 degree 60s exposures 
empirically, in real practice, equivalent statistically to six passes with 0.5 
degree 10s frames? Better? Worse? Our home source has been donated away to 
Connecticut, so I can't do this experiment myself anymore.

All the best,

Jacob Keller


***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***